kfukuta/wf-transcriptomes-v202
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Merge branch 'CW-3244' into 'dev'

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change significance level to mark on MA plot

Closes CW-3244

See merge request epi2melabs/workflows/wf-transcriptomes!164
This commit is contained in:
Sarah Griffiths 2024-04-10 08:09:23 +00:00
commit 6f2ac3241b
2 changed files with 16 additions and 1 deletions
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4
CHANGELOG.md
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@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [unreleased]
### Changed
- MA plot in the `results_dge.pdf` has been updated to match the MA plot in the report.
## [v1.1.1] ## [v1.1.1]
### Changed ### Changed
- Improved handling of different annotation file types (eg. `.gtf/.gff/.gff3`) in `de_analysis` mode. - Improved handling of different annotation file types (eg. `.gtf/.gff/.gff3`) in `de_analysis` mode.

13
bin/de_analysis.R
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@ -123,7 +123,18 @@ qlf <- glmQLFTest(fit)
edger_res <- topTags(qlf, n=nrow(y), sort.by="PValue")[[1]] edger_res <- topTags(qlf, n=nrow(y), sort.by="PValue")[[1]]
pdf("de_analysis/results_dge.pdf") pdf("de_analysis/results_dge.pdf")
plotMD(qlf)
# create status vector
status <- ifelse(
qlf$PValue<0.01 & qlf$logFC>0,
'up',
ifelse(
qlf$PValue<0.01 & qlf$logFC<=0,
'down',
'notsig'
)
)
plotMD(qlf, status=status, values=c("up","down","notsig"), hl.col=c("red","blue","black"))
abline(h=c(-1,1), col="blue") abline(h=c(-1,1), col="blue")
plotQLDisp(fit) plotQLDisp(fit)